Totemic former skipper Leitch will line up at number eight to win his 90th cap, while Gunter starts at blindside flanker with Kanji Shimokawa on the openside.
Gunter is one of four Australian-raised players in the matchday squad along with centre Dylan Riley, lock Jack Cornelsen and replacement outside back Sam Greene.
In other changes from the Brave Blossoms team that lost to Fiji in the Pacific Nations Cup final last month, Yoshitaka Yazaki starts at fullback and Kippei Ishida returns on the right wing.
Tomoki Osada swaps over to the left wing and Shogo Nakano partners Riley in the centres with Charlie Lawrence dropping to the bench.
Captain Warner Dearns will pack down in the second row with Cornelsen, while Lee Seung-sin retains the flyhalf spot to win his 25th cap as playmaker.
Joe Schmidt earlier announced 13 changes to Australia's starting side and a new captain for the matchup against Jones, his predecessor as Wallabies coach.
Japan have never beaten Australia in six previous attempts.
Japan team to face Australia:
Backs: 15–Yoshitaka Yazaki, 14–Kippei Ishida, 13–Dylan Riley, 12–Shogo Nakano, 11–Tomoki Osada, 10–Lee Seung-sin, 9–Shinobu Fujiwara,
Forwards: 8–Michael Leitch, 7–Kanji Shimokawa, 6–Ben Gunter, 5–Warner Dearns, 4–Jack Cornelsen, 3–Shuhei Takeuchi, 2–Hayate Era, 1–Kenta Kobayashi
Replacements: 16–Kenji Sato, 17–Ryosuke Iwaihara, 18–Keijiro Tamefusa, 19–Tyler Paul, 20–Tiennan Costley, 21–Kenta Fukuda, 22–Charlie Lawrence, 23–Sam Greene
